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samtools-coverage(1)	     Bioinformatics tools	  samtools-coverage(1)

NAME
       samtools	coverage - produces a histogram	or table of coverage per chro-
       mosome

SYNOPSIS
       samtools	      coverage	     [options]	     [in1.sam|in1.bam|in1.cram
       [in2.sam|in2.bam|in2.cram] [...]]

DESCRIPTION
       Computes	 the  depth  at	each position or region	and draws an ASCII-art
       histogram or tabulated text.

       The tabulated form uses the following headings.

       rname	   Reference name / chromosome
       startpos	   Start position
       endpos	   End position	(or sequence length)
       numreads	   Number reads	aligned	to the region (after filtering)
       covbases	   Number of covered bases with	depth >= 1
       coverage	   Proportion of covered bases [0..1]
       meandepth   Mean	depth of coverage
       meanbaseq   Mean	baseQ in covered region
       meanmapq	   Mean	mapQ of	selected reads

OPTIONS
       Input options:

       -b, --bam-list FILE
	       List of input BAM files,	one file per line [null]

       -l, --min-read-len INT
	       Ignore reads shorter than INT base pairs	[0]

       -q, --min-MQ INT
	       Minimum mapping quality for an alignment	to be used [0]

       -Q, --min-BQ INT
	       Minimum base quality for	a base to be considered	[0]

       --rf, --incl-flags STR|INT
	       Required	flags: skip reads with mask bits unset [null]

       --ff, --excl-flags STR|INT
	       Filter  flags:  skip  reads  with  mask	bits  set  [UNMAP,SEC-
	       ONDARY,QCFAIL,DUP]

       Output options:

       -m, --histogram
	       Show histogram instead of tabular output.

       -A, --ascii
	       Show only ASCII characters in histogram.

       -o, --output FILE
	       Write output to FILE [stdout].

       -H, --no-header
	       Don't print a header in tabular mode.

       -w, --n-bins INT
	       Number of bins in histogram.  [terminal width - 40]

       -r, --region REG
	       Show specified region. Format: chr:start-end.

       -h, --help
	       Shows command help.

EXAMPLES
       Running coverage	in tabular mode, on a specific region, with tabs shown
       as spaces for clarity in	this man page.

	 samtools coverage -r chr1:1M-12M input.bam

	 #rname	 startpos  endpos    numreads  covbases	 coverage  meandepth  meanbaseq	 meanmapq
	 chr1	 1000000   12000000  528695    1069995	 9.72723   3.50281    34.4	 55.8

       An example of the histogram output is below, with ASCII	block  charac-
       ters replaced by	"#" for	rendering in this man page.

	 samtools coverage -A -w 32 -r chr1:1M-12M input.bam

	 chr1 (249.25Mbp)
	 >  24.19% | #				    | Number of	reads: 528695
	 >  21.50% |##				    |	  (132000 filtered)
	 >  18.81% |##				    | Covered bases:   1.07Mbp
	 >  16.12% |##				 #  | Percent covered: 9.727%
	 >  13.44% |##	#  #	   ##		 # #| Mean coverage:   3.5x
	 >  10.75% |## ##  #	   ##	       # # #| Mean baseQ:      34.4
	 >   8.06% |#####  #	   ##	     # # # #| Mean mapQ:       55.8
	 >   5.37% |##### ##	  ###	   # ##### #|
	 >   2.69% |##### ###	  ###  ### #########| Histo bin	width: 343.8Kbp
	 >   0.00% |############ ###################| Histo max	bin:   26.873%
		 1.00M	   4.44M     7.87M	 12.00M

AUTHOR
       Written by Florian P Breitwieser.

SEE ALSO
       samtools(1), samtools-depth(1),

       Samtools	website: <http://www.htslib.org/>

samtools-1.11		       22 September 2020	  samtools-coverage(1)

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | EXAMPLES | AUTHOR | SEE ALSO

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